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1dek

From Proteopedia

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{{Seed}}
 
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[[Image:1dek.png|left|200px]]
 
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<!--
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==DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP==
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The line below this paragraph, containing "STRUCTURE_1dek", creates the "Structure Box" on the page.
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<StructureSection load='1dek' size='340' side='right'caption='[[1dek]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1dek]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DEK FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGP:2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>DGP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene></td></tr>
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{{STRUCTURE_1dek| PDB=1dek | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dek OCA], [https://pdbe.org/1dek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dek RCSB], [https://www.ebi.ac.uk/pdbsum/1dek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dek ProSAT]</span></td></tr>
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</table>
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===DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP===
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== Function ==
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[https://www.uniprot.org/uniprot/DNMK_BPT4 DNMK_BPT4] Phosphorylates dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP. The phosphorylation of 5-hydroxymethyl-dCMP represents the first step in the replacement of cytosine by hydroxymethylcytosine in new viral DNA genomes.<ref>PMID:5338507</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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The line below this paragraph, {{ABSTRACT_PUBMED_8670851}}, adds the Publication Abstract to the page
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Check<jmol>
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(as it appears on PubMed at http://www.pubmed.gov), where 8670851 is the PubMed ID number.
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/de/1dek_consurf.spt"</scriptWhenChecked>
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{{ABSTRACT_PUBMED_8670851}}
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==About this Structure==
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</jmolCheckbox>
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1DEK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DEK OCA].
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dek ConSurf].
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<div style="clear:both"></div>
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==Reference==
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== References ==
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Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP., Teplyakov A, Sebastiao P, Obmolova G, Perrakis A, Brush GS, Bessman MJ, Wilson KS, EMBO J. 1996 Jul 15;15(14):3487-97. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8670851 8670851]
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<references/>
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[[Category: Enterobacteria phage t4]]
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__TOC__
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[[Category: Single protein]]
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</StructureSection>
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[[Category: Sebastiao, P.]]
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[[Category: Escherichia virus T4]]
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[[Category: Teplyakov, A.]]
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[[Category: Large Structures]]
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[[Category: Phosphotransferase]]
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[[Category: Sebastiao P]]
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[[Category: Transferase]]
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[[Category: Teplyakov A]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 22:54:33 2008''
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Current revision

DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP

PDB ID 1dek

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